Insights from a 3-Year Genomic Evolution of SARS-CoV-2 Shows a Predominance of Variants from Developing Countries (preprint)

Since the emergence of SARS-CoV-2, the virus has rapidly disseminated globally, with consequential genetic changes that have profoundly affected its pathogenicity, transmissibility, and immune evasion. Therefore, the pressing need to gain a comprehensive understanding of the genetic evolution and dissemination of this virus across diverse regions is paramount. In light of this, the present study aimed to investigate the spatial and temporal distribution of SARS-CoV-2 variants by leveraging genomic sequencing data. We analyzed a representative dataset of 14,759 genomic sequences of SARS-CoV-2 obtained from 142 countries, spanning the period from January 2020 to January 2023. The findings showed that the early spread of certain SARS-CoV-2 lineages was geographically limited. However, the subsequent lifting of quarantine and travel restrictions facilitated the homogenization of the virus' genetic diversity across diverse regions. Moreover, our temporal analysis demonstrated that the lifespan of SARS-CoV-2 variants has been significantly truncated over time, with dominant strains frequently being outcompeted by more adaptive variants. We further observed that a significant proportion of newly emerged SARS-CoV-2 variants were identified in developing countries, particularly in sub-Saharan Africa, South America, and South Asia. Lastly, our results underscore the impact of weakened health systems, a high prevalence of immunocompromised individuals, and delayed reporting of these variants on the spread and severity of the virus in these regions.

Evaluation of the MAScIR SARS-CoV-2 M Kit 2.0 on the SARS-CoV-2 Infection.

SARS-CoV-2 is a major public health problem worldwide. Since its emergence, several diagnostic kits have been developed to ensure rapid patient management. The aim of our study is to check the performance of the new Moroccan SARS-CoV-2 detection kit: MAScIR SARS-CoV-2 M 2.0. The following parameters were studied: repeatability, reproducibility, analytical specificity, analytical sensitivity, and comparison with the GeneFinder™ COVID-19 Plus RealAmp Kit. In addition, an external quality evaluation comprising five specimens was carried out as part of an international program for the external quality evaluation of sublaboratories of the WHO and the Laboratory Office of the National Institute of Hygiene of Morocco. The results of all parameters studied showed an analytical performance that complied with the requirements of the method verification/validation protocol adopted by the Central Laboratory of Virology and met the recommendations of COFRAC (French Accreditation Committee). During the current study, the sequencing of some randomly selected positive samples was performed, among which the carriers of the Alpha variant, the Delta variant, and the Omicron variant were detected. These results allowed us to deduce that this kit was valid for detecting these three variants.

Phylogeography and genomic analysis of SARS-CoV-2 delta variant in Morocco.

INTRODUCTION: Since the COVID-19 pandemic began in December 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continuously evolved with many variants of concern emerging across the world. METHODOLOGY: In order to monitor the evolution of these variants in Morocco, we analyzed a total of 2130 genomes of the delta variant circulating around the world. We also included 164 Moroccan delta variant sequences in our analysis. RESULTS: Our findings suggest at least four introductions from multiple international sources and a rise of a dominant delta sub-lineage AY.33 in Morocco. Moreover, we report three mutations in the N-terminal domain of the S protein specific to the Moroccan AY.33 isolates, T29A, T250I and T299I. The effect of these mutations on the secondary structure and the dynamic behavior of the S protein N-terminal domain was further determined. CONCLUSIONS: We conclude that these mutations might have functional consequences on the S protein of SARS-CoV-2.

Report of SARS-CoV-2 BA.1 Lineage in Morocco.

Here, we report the near-complete genome sequence and genetic variations of a clinical sample of SARS-CoV-2 for the newly emerged Omicron variant (BA.1). The sample was collected from a nasopharyngeal swab of a Moroccan patient, and the sequencing was done using Ion S5 technology.

IDbSV: An Open-Access Repository for Monitoring SARS-CoV-2 Variations and Evolution.

Ending COVID-19 pandemic requires a collaborative understanding of SARS-CoV-2 and COVID-19 mechanisms. Yet, the evolving nature of coronaviruses results in a continuous emergence of new variants of the virus. Central to this is the need for a continuous monitoring system able to detect potentially harmful variants of the virus in real-time. In this manuscript, we present the International Database of SARS-CoV-2 Variations (IDbSV), the result of ongoing efforts in curating, analyzing, and sharing comprehensive interpretation of SARS-CoV-2's genetic variations and variants. Through user-friendly interactive data visualizations, we aim to provide a novel surveillance tool to the scientific and public health communities. The database is regularly updated with new records through a 4-step workflow (1-Quality control of curated sequences, 2-Call of variations, 3-Functional annotation, and 4-Metadata association). To the best of our knowledge, IDbSV provides access to the largest repository of SARS-CoV-2 variations and the largest analysis of SARS-CoV-2 genomes with over 60 thousand annotated variations curated from the 1,808,613 genomes alongside their functional annotations, first known appearance, and associated genetic lineages, enabling a robust interpretation tool for SARS-CoV-2 variations to help understanding SARS-CoV-2 dynamics across the world.

A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa.

The progression of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in Africa has so far been heterogeneous, and the full impact is not yet well understood. In this study, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations predominantly from Europe, which diminished after the early introduction of international travel restrictions. As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and spread within the continent of many variants of concern and interest, such as B.1.351, B.1.525, A.23.1, and C.1.1. Although distorted by low sampling numbers and blind spots, the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a source for new variants.

In silico analysis of ACE2 orthologues to predict animal host range with high susceptibility to SARS-CoV-2.

SARS-CoV-2, which causes severe pneumonia epidemics, probably originated from Chinese horseshoe bats, but the intermediate and host range is still unknown. ACE2 is the entry receptor for SARS-CoV-2. The binding capacity of SARS-CoV-2 spike protein to ACE2 is the critical determinant of viral host range and cross-species infection. Here, we used an in silico approach to predict the potential animals range with high susceptibility to SARS-CoV-2 by modelling and studying the Spike-ACE2 interaction of 22 domestic and wild animals. Our results showed that all studied animals are potentially susceptible to SARS-CoV-2 infection with a slight difference in the binding affinity and stability of their ACE2-RBD complexes. Furthermore, we identified a specific substitution of tyrosine to histidine at position 41 in ACE2 that likely reduces the affinity to SARS-CoV-2 in horses and greater horseshoe bats. These results may help to provide important insights into SARS-CoV-2 host range which will make it possible to control the spread of the virus and identify animal models that could be used for screening antiviral drugs or vaccine candidates against SARS-CoV-2.

Report of SARS-CoV-2 B1.1.7 Lineage in Morocco.

Here, we report the near-complete genome sequence and the genetic variations of a clinical sample of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) harboring the N501Y mutation assigned to the B.1.1.7 lineage. The sample was collected from a nasopharyngeal swab of a female patient from Temara, Morocco, and the sequencing was done using Ion S5 technology.

First Report of a SARS-CoV-2 Genome Sequence with a Spike His69-Val70 Deletion and an Asn439Lys Mutation in Morocco.

We report the nearly complete genome sequence and the genetic variations of a clinical sample of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) collected from a nasopharyngeal swab specimen from a male patient from Harhoura-Rabat, Morocco. The sequence, which was obtained using Ion Torrent technology, is valuable as it carries a recently described deletion (His69-Val70) and substitution (Asn439Lys).

Identifying epitopes for cluster of differentiation and design of new peptides inhibitors against human SARS-CoV-2 spike RBD by an in-silico approach.

The coronavirus disease 19 (COVID-19) is a highly contagious and rapidly spreading infection caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In some cases, the disease can be fatal which resulted in more than one million deaths worldwide according the WHO. Currently, there is no effective vaccine or treatment for COVID-19, however many small-molecule inhibitors have shown potent antiviral activity against SARS-CoV-2 and some of them are now under clinical trials. Despite their promising activities, the development of these small molecules for the clinical use can be limited by many factors like the off-target effect, the poor stability, and the low bioavailability. The clusters of differentiation CD147, CD209, CD299 have been identified as essential entry co-receptors for SARS-CoV-2 species specificity to humans, although the underlying mechanisms are yet to be fully elucidated. In this paper, protein-protein docking was utilized for identifying the critical epitopes in CD147, CD209 and CD299 which are involved in the binding with SARS-CoV-2 Spike receptor binding domain (RBD). The results of binding free energies showed a high affinity of SARS-CoV-2 RBD to CD299 receptor which was used as a reference to derive hypothetical peptide sequences with specific binding activities to SARS-CoV-2 RBD. Molecular docking and molecular dynamics simulations of the newly designed peptides showed favorable binding features and stability with SARS-CoV-2 RBD and therefore can be further considered as potential candidates in future anti-SARS CoV-2 drug discovery studies.

Large scale genomic analysis of 3067 SARS-CoV-2 genomes reveals a clonal geo-distribution and a rich genetic variations of hotspots mutations.

In late December 2019, an emerging viral infection COVID-19 was identified in Wuhan, China, and became a global pandemic. Characterization of the genetic variants of SARS-CoV-2 is crucial in following and evaluating it spread across countries. In this study, we collected and analyzed 3,067 SARS-CoV-2 genomes isolated from 55 countries during the first three months after the onset of this virus. Using comparative genomics analysis, we traced the profiles of the whole-genome mutations and compared the frequency of each mutation in the studied population. The accumulation of mutations during the epidemic period with their geographic locations was also monitored. The results showed 782 variants sites, of which 512 (65.47%) had a non-synonymous effect. Frequencies of mutated alleles revealed the presence of 68 recurrent mutations, including ten hotspot non-synonymous mutations with a prevalence higher than 0.10 in this population and distributed in six SARS-CoV-2 genes. The distribution of these recurrent mutations on the world map revealed that certain genotypes are specific to geographic locations. We also identified co-occurring mutations resulting in the presence of several haplotypes. Moreover, evolution over time has shown a mechanism of mutation co-accumulation which might affect the severity and spread of the SARS-CoV-2. The phylogentic analysis identified two major Clades C1 and C2 harboring mutations L3606F and G614D, respectively and both emerging for the first time in China. On the other hand, analysis of the selective pressure revealed the presence of negatively selected residues that could be taken into considerations as therapeutic targets. We have also created an inclusive unified database (http://covid-19.medbiotech.ma) that lists all of the genetic variants of the SARS-CoV-2 genomes found in this study with phylogeographic analysis around the world.

Genomic Diversity and Hotspot Mutations in 30,983 SARS-CoV-2 Genomes: Moving Toward a Universal Vaccine for the "Confined Virus"?

The COVID-19 pandemic has been ongoing since its onset in late November 2019 in Wuhan, China. Understanding and monitoring the genetic evolution of the virus, its geographical characteristics, and its stability are particularly important for controlling the spread of the disease and especially for the development of a universal vaccine covering all circulating strains. From this perspective, we analyzed 30,983 complete SARS-CoV-2 genomes from 79 countries located in the six continents and collected from 24 December 2019, to 13 May 2020, according to the GISAID database. Our analysis revealed the presence of 3206 variant sites, with a uniform distribution of mutation types in different geographic areas. Remarkably, a low frequency of recurrent mutations has been observed; only 169 mutations (5.27%) had a prevalence greater than 1% of genomes. Nevertheless, fourteen non-synonymous hotspot mutations (>10%) have been identified at different locations along the viral genome; eight in ORF1ab polyprotein (in nsp2, nsp3, transmembrane domain, RdRp, helicase, exonuclease, and endoribonuclease), three in nucleocapsid protein, and one in each of three proteins: Spike, ORF3a, and ORF8. Moreover, 36 non-synonymous mutations were identified in the receptor-binding domain (RBD) of the spike protein with a low prevalence (<1%) across all genomes, of which only four could potentially enhance the binding of the SARS-CoV-2 spike protein to the human ACE2 receptor. These results along with intra-genomic divergence of SARS-CoV-2 could indicate that unlike the influenza virus or HIV viruses, SARS-CoV-2 has a low mutation rate which makes the development of an effective global vaccine very likely.

Targeting the GRP78-Dependant SARS-CoV-2 Cell Entry by Peptides and Small Molecules.

The global burden of infections and the rapid spread of viral diseases show the need for new approaches in the prevention and development of effective therapies. To this end, we aimed to explore novel inhibitor compounds that can stop replication or decrease the viral load of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), for which there is currently no approved treatment. Besides using the angiotensin-converting enzyme (ACE2) receptor as a main gate, the CoV-2 can bind to the glucose-regulating protein 78 (GRP78) receptor to get into the cells to start an infection. Here, we report potential inhibitors comprising small molecules and peptides that could interfere with the interaction of SARS-CoV-2 and its target cells by blocking the recognition of the GRP78 cellular receptor by the viral Spike protein. These inhibitors were discovered through an approach of in silico screening of available databases of bioactive peptides and polyphenolic compounds and the analysis of their docking modes. This process led to the selection of 9 compounds with optimal binding affinities to the target sites. The peptides (satpdb18674, satpdb18446, satpdb12488, satpdb14438, and satpdb28899) act on regions III and IV of the viral Spike protein and on its binding sites in GRP78. However, 4 polyphenols such as epigallocatechin gallate (EGCG), homoeriodictyol, isorhamnetin, and curcumin interact, in addition to the Spike protein and its binding sites in GRP78, with the ATPase domain of GRP78. Our work demonstrates that there are at least 2 approaches to block the spread of SARS-CoV-2 by preventing its fusion with the host cells via GRP78.

Repurposing of known anti-virals as potential inhibitors for SARS-CoV-2 main protease using molecular docking analysis.

The new SARS-CoV-2 coronavirus is the causative agent of the COVID-19 pandemic outbreak that affected more than 190 countries worldwide with more than 292,000 confirmed cases and over 12,700 deaths. There is at the moment no vaccine or effective treatment for this disease which constitutes a serious global health problem. It is of interest to use a structure based virtual screening approach for the identification of potential inhibitors of the main protease of SARS-CoV-2 (Mpro) from antiviral drugs used to treat other viral disease such as human immunodeficiency virus (HIV) and hepatitis C virus (HCV) infections. The crystallographic structure with PDB ID: 6LU7 of Mpro in complex with the inhibitor N3 was used as a model in the virtual screening of 33 protease inhibitors collected from the ChEMBL chemical database. Molecular docking analysis was performed using the standard AutoDock vina protocol followed by ranking and selection of compounds based on their binding affinity. We report 10 candidates with optimal binding features to the active site of the protease for further consideration as potential drugs to treat patients infected with the emerging COVID-19 disease.

Genome Sequences of Six SARS-CoV-2 Strains Isolated in Morocco, Obtained Using Oxford Nanopore MinION Technology.

Here, we report the draft genome sequences of six severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains. SARS-CoV-2 is responsible for the COVID-19 pandemic, which started at the end of 2019 in Wuhan, China. The isolates were obtained from nasopharyngeal swabs from Moroccan patients with COVID-19. Mutation analysis revealed the presence of the spike D614G mutation in all six genomes, which is widely present in several genomes around the world.